Antigen Tracking Figures
Ryan Sheridan
2024-01-02
Figure 1
Antigen persists in discrete cell populations within the lymph node
- Experimental design
- Mean Ag-score is shown for each cell type for 2, 14, 21, and 42 days post vaccination.
- UMAP projection shows LEC subsets.
- UMAP projections show Ag-scores for LEC subsets for each timepoint.
- Mean Ag-score is shown for LEC subsets for each timepoint.
- Ag-scores are shown for each timepoint for each LEC subset.
- UMAP projection shows DC subsets.
- UMAP projections show Ag-scores for DC subsets for each timepoint.
- Mean Ag-score is shown for DC subsets for each timepoint.
- Ag-scores are shown for each timepoint for each DC subset.
Notes
- Experiment 1 is shown for the LEC 21 and 42 day timepoints. Experiment 2 data include very few LECs for the 21 day timepoint.
- Experiment 2 is shown for the DC 21 and 42 day timepoints. Experiment 1 data are lower quality (sparse signal, mostly zeros).
- Subsets are only shown if there are >= 5 cells for each timepoint
- CD45+ and CD45- cell types are only shown for the CD45+ and CD45- datasets, respectively.
Figure 2
Identification of an antigen archiving gene signature
- Ag-score is shown for day 14 Ag-high and -low cells identified for LEC subsets with the highest Ag-score.
- The fraction of cells predicted to be Ag-competent is shown for each LEC subset 14, 21, and 42 days post vaccination.
- Ag-high module score is shown for Ag-high and predicted Ag-competent LECs for each timepoint. P values were calculated by pooling cells from all three timepoints for each Ag class. P values were calculated using a one-sided t test with Bonferroni correction to compare Ag-high vs Ag-competent and Ag-competent vs Ag-low cells for each LEC subset.
- UMAP projections show cLEC Ag-high module scores for each timepoint.
- The expression of select genes from the Ag-high (top four) and Ag-low (bottom four) gene modules is shown for cLECs. Genes identified as top predictors for all three LEC subsets are shown.
Notes
- Ag-low and -high cells were identified by separately clustering each d14 LEC subset for each sample into two groups based on Ag-score.
- The cutoffs identified for the d14 dataset were then used to identify Ag-high cells for the other timepoints.
- With this approach there is a different cutoff for each LEC subset, but the cutoff is consistent across timepoints.
Figure 3
Antigen archiving is enhanced by successive vaccinations
- Mean 21 day Ag-score is shown for LECs from mice that received a single vaccination (21 day or 42 day) or dual vaccination (21 day and 42 day).
- UMAP projections show 21 day Ag-scores for LEC subsets for single and dual vaccinations.
- Prior vaccination enhances antigen archiving. Ag-score is shown for single and dual vaccinations for the 21 day timepoint for each LEC subset. Other timepoints are shown in grey. P values were calculated using a one-sided t test with Bonferroni correction.
- Mean 42 day Ag-score is shown as described in A.
- UMAP projections show 42 day Ag-scores for LEC subsets as described in B.
- Successive vaccinations enhances retention of previously archived antigen. Ag-score is shown for the 42 day timepoint as described in C.
- 21 day and 42 day Ag-score is compared for each LEC subset.
- Ag-high module scores described in Figure 2 are shown for LECs that archived antigens from both vaccinations (double-high), from only one vaccination (single-high), or have low levels of both antigens (Ag-low).
Notes
- H shows that the best archivers (the ones that archive Ag from both vaccinations) show strongest expression of the Ag-high gene modules. Need to add p values.
Figure 4
Antigen uptake by DCs is enhanced by successive vaccinations
- Mean 21 day Ag-score is shown for DCs from mice that received a single vaccination (21 day or 42 day) or dual vaccination (21 day and 42 day).
- Ag-score is shown for single and dual vaccinations for the 21 day timepoint for DC subsets with highest Ag-score. Other timepoints are shown in grey. P values were calculated using a one-sided t test with Bonferroni correction.
- Mean 42 day Ag-score is shown for DCs from mice that received single or dual vaccination as described in A.
- Ag-score is shown for single and dual vaccinations for the 42 day timepoint as described in B.
Notes
- Need to add GeoMx figures showing Ag signal is highest in medula and sinus regions for both LECs and DCs.
Figure 5
Antigen archiving is impaired during CHIKV infection
- UMAP projections show LEC subsets for mock and CHIKV-infected mice.
- UMAP projections show predicted Ag-competent cLECs for mock and CHIKV-infected mice.
- The fraction of predicted Ag-competent cLECs is shown for mock and CHIKV-infected mice for each biological replicate.
- UMAP projections show cLEC Ag-high module scores for mock and CHIKV-infected mice.
- cLEC Ag-high module scores are shown for mock and CHIKV-infected mice for each biological replicate.
- Expression of cLEC Ag-high gene module is shown for mock and CHIKV-infected mice for top LEC subsets.
Notes
- Need to add p values for C and E.
- Predicted Ag-competent fLECs and collecting LECs can be shown as a supplemental figure (no difference between mock and CHIKV).
